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Forum: Illumina/Solexa 11-06-2019, 06:45 PM
Replies: 18
Views: 852
Posted By samd
Hi itstrieu, I see. Well I guess I am...

Hi itstrieu,

I see. Well I guess I am getting very low outputs then.. I will run that suggestion by them. It is just strange because my first run at Berkeley which I consider "good" was done at...
Forum: Illumina/Solexa 11-06-2019, 04:21 PM
Replies: 18
Views: 852
Posted By samd
Ok so I am guessing the "25M total reads" on...

Ok so I am guessing the "25M total reads" on Basespace actually means 50M since I did PE. Thanks for the suggestion I will look into that.

One thing I just remembered is the QC results were quite...
Forum: Sample Prep / Library Generation 11-06-2019, 04:13 PM
Replies: 2
Views: 328
Posted By samd
discrepancy in miseq runs due to sample prep protocol?

Hi all,

I have had an issue where my first ever Miseq run was great quality: 100k reads per sample with a nice distribution and then after switching sequencing facilities I get lower outputs and...
Forum: Illumina/Solexa 11-06-2019, 02:54 PM
Replies: 18
Views: 852
Posted By samd
Hi SNPsaurus, Interesting. I have heard of...

Hi SNPsaurus,

Interesting. I have heard of the spacer primers but I think I am past the point in my PhD of redoing everything. But it would be nice.

This might be a dumb question but I thought...
Forum: Illumina/Solexa 11-06-2019, 02:43 PM
Replies: 18
Views: 852
Posted By samd
Hi nucacidhunter, Sorry do you mean manually...

Hi nucacidhunter,

Sorry do you mean manually changing the cluster density to 800k/mm2? Is this something I could tell the facility to do?
And I have been using Ilumina UD indexes so I am guessing...
Forum: Illumina/Solexa 11-06-2019, 02:27 PM
Replies: 18
Views: 852
Posted By samd
Hi SNPsaurus, Ok so after discussing with...

Hi SNPsaurus,

Ok so after discussing with them the 11M reads simply referred to the forward reads. The 23M PF refers to the forward and reverse. I see a 40% undetermined reads metric. Which is a...
Forum: Illumina/Solexa 11-06-2019, 10:29 AM
Replies: 18
Views: 852
Posted By samd
Hi GenoMax, Under the Indexing QC tab it...

Hi GenoMax,

Under the Indexing QC tab it says Total Reads: 25,058,484 and then PF Reads: 23,419,084. And then the density is at 477. I believe this would be total reads: R1 +R2?
However, when I...
Forum: Illumina/Solexa 11-06-2019, 10:22 AM
Replies: 18
Views: 852
Posted By samd
@luc I used the Ilumina unique dual indexes...

@luc

I used the Ilumina unique dual indexes so that should not be an issue right?

@SNPsaurus

I have not done that. I know that is much more accurate we just don't exactly have the...
Forum: Illumina/Solexa 11-06-2019, 10:15 AM
Replies: 18
Views: 852
Posted By samd
Hi all, appreciate the responses ...

Hi all,
appreciate the responses

@nucacidhunter
1. Primers are the EMP 515-806 V4 region
2. Cluster density was about 477 if I remember correctly
3. Just 1 library. Usually I was doing 160...
Forum: Illumina/Solexa 11-04-2019, 08:30 PM
Replies: 18
Views: 852
Posted By samd
Low data output from questionable sequencing facility

Hi all,

I have been getting some questionable runs from a sequencing facility and was wondering if there could be any clues as to whether it is their fault or my own fault in lab prep.

I am...
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